Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE CLASS A BETA-LACTAMASE PENL-TTR11 CONTAINING 20 RESIDUES INSERTION IN OMEGA-LOOP
 
Authors :  J. M. Choi, H. Yi, H. S. Kim, S. H. Lee
Date :  10 Jul 16  (Deposition) - 15 Feb 17  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta0Lactamase, Penl-Ttr11, Omega-Loop, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Yi, J. M. Choi, J. Hwang, F. Prati, T. P. Cao, S. H. Lee, H. S. Kim
High Adaptability Of The Omega Loop Underlies The Substrate-Spectrum-Extension Evolution Of A Class A Beta-Lactamase, Penl
Sci Rep V. 6 36527 2016
PubMed-ID: 27827433  |  Reference-DOI: 10.1038/SREP36527

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    ChainsA
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A(+)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 31-294
    GeneBLA, DR63_4327
    Organism ScientificBURKHOLDERIA THAILANDENSIS
    Organism Taxid271848
    StrainATCC 700388 / DSM 13276 / CIP 106301 / E264

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5GLC)

(-) Sites  (0, 0)

(no "Site" information available for 5GLC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GLC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GLC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GLC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GLC)

(-) Exons   (0, 0)

(no "Exon" information available for 5GLC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh..hhhhhh.eeeehhhhh.....hhhhhheeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5glc A  22 GSHMRNVAAEQQLRELESTFDGRLGFVALDTATGARIAHRADERFPFCSTFKTMLSAAVLARSAGDAALLQRRIPYAKRDLVRYSPITEKHVGAGMTVAELCAATLQYSDNTAANLLIALLGGPQAVTAYARSIGDATFRLDLPGDERDTTTPAAMAASVRRLLVGDALGTAQRAQLNAWMLGNKTGDARIRAGVPAGWRVADKTGTGDYGTGNDIGVAYPPDRAPIVFVVYTTMRSRNAQARDDVIASAARIAARAFV 311
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161 ||    200       210       220       230       240       250       261       271||     282       292       302         
                                                                                                                                                                       163|                                                              258|         272|                                     
                                                                                                                                                                        193                                                               260          274                                     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GLC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GLC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GLC)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5glc)
 
  Sites
(no "Sites" information available for 5glc)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5glc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5glc
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q2T5A3_BURTA | Q2T5A3
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.5.2.6
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q2T5A3_BURTA | Q2T5A3
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q2T5A3_BURTA | Q2T5A35gl9 5gla 5glb 5gld

(-) Related Entries Specified in the PDB File

5gl9 5gla 5glb 5gld